Variant report

Variant	nsv596172
Chromosome Location	chr4:172213470-172243508
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:172215140-172215290	HCM	heart:	n/a	n/a
2	CTCF	chr4:172226360-172226510	MCF-7	breast:	n/a	n/a
3	CTCF	chr4:172230160-172230310	MCF-7	breast:	n/a	n/a
4	CTCF	chr4:172223289-172223339	LNCaP	prostate:	n/a	n/a
5	CUX1	chr4:172237445-172237450	K562	blood:	n/a	n/a
6	E2F4	chr4:172224413-172224425	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL2	chr4:172220041-172220338	HepG2	liver:	n/a	n/a
8	FOXA1	chr4:172229823-172230149	T-47D	breast:	n/a	chr4:172230046-172230061
9	FOXA1	chr4:172229889-172230180	HepG2	liver:	n/a	chr4:172230046-172230061
10	FOXA1	chr4:172229887-172230167	T-47D	breast:	n/a	chr4:172230046-172230061
11	FOXA1	chr4:172229918-172230175	HepG2	liver:	n/a	chr4:172230046-172230061
12	FOXA2	chr4:172229869-172230113	HepG2	liver:	n/a	n/a
13	IRF1	chr4:172238010-172238045	K562	blood:	n/a	n/a
14	MAFK	chr4:172214202-172214353	HepG2	liver:	n/a	n/a
15	MAFK	chr4:172227335-172227455	HepG2	liver:	n/a	n/a
16	MYC	chr4:172216406-172216595	MCF10A-Er-Src	breast:	n/a	n/a
17	NFYA	chr4:172220037-172220290	K562	blood:	n/a	n/a
18	NFYB	chr4:172220041-172220286	GM12878	blood:	n/a	n/a
19	NFYB	chr4:172220032-172220410	K562	blood:	n/a	n/a
20	POLR2A	chr4:172241292-172241380	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:172214408-172214568	MCF10A-Er-Src	breast:	n/a	n/a
22	SP1	chr4:172220102-172220368	HepG2	liver:	n/a	n/a
23	SPI1	chr4:172232928-172233193	HL-60	blood:	n/a	n/a
24	SPI1	chr4:172232947-172233169	GM12891	blood:	n/a	n/a
25	SPI1	chr4:172232968-172233163	GM12878	blood:	n/a	n/a
26	SPI1	chr4:172233024-172233142	K562	blood:	n/a	n/a
27	STAT3	chr4:172216254-172216588	MCF10A-Er-Src	breast:	n/a	chr4:172216354-172216365

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:172219751-172219801	SK-N-MC	brain:	n/a
2	chr4:172219751-172219801	Jurkat	blood:	n/a
3	chr4:172219751-172219801	AG04449	skin:	fetal
4	chr4:172219751-172219801	HNPCEpiC	eye:	n/a
5	chr4:172219751-172219801	NT2-D1	testis:	n/a
6	chr4:172219751-172219801	ECC-1	luminal epithelium:	n/a
7	chr4:172219751-172219801	HCT-116	colon:	n/a
8	chr4:172219751-172219801	Caco-2	colon:	n/a
9	chr4:172219751-172219801	AG09319	gingival:	n/a
10	chr4:172219751-172219801	SK-N-SH_RA	brain:	n/a
11	chr4:172219751-172219801	LNCaP	prostate:	n/a
12	chr4:172219751-172219801	GM12878	blood:	n/a
13	chr4:172219751-172219801	GM12892	blood:	n/a
14	chr4:172219751-172219801	K562	blood:	n/a
15	chr4:172219751-172219801	HIPEpiC	eye:	n/a
16	chr4:172219751-172219801	SAEC	small airway:	n/a
17	chr4:172219751-172219801	SK-N-SH	brain:	n/a
18	chr4:172219751-172219801	GM06990	blood:	n/a
19	chr4:172219751-172219801	NH-A	brain:	n/a
20	chr4:172219751-172219801	IMR90	lung:	fetal
21	chr4:172219751-172219801	AG04450	lung:	fetal
22	chr4:172219751-172219801	HRCEpiC	kidney:	n/a
23	chr4:172219751-172219801	HepG2	liver:	n/a
24	chr4:172219751-172219801	SKMC	muscle:	n/a
25	chr4:172219751-172219801	MCF10A-Er-Src	breast:	n/a
26	chr4:172219751-172219801	AoSMC	blood vessel:	n/a
27	chr4:172219751-172219801	HCPEpiC	choroid plexus:	n/a
28	chr4:172219751-172219801	H1-hESC	embryonic stem cell:	embryo
29	chr4:172219751-172219801	Hepatocyte	liver:	n/a
30	chr4:172219751-172219801	AG09309	skin:	n/a
31	chr4:172219751-172219801	PANC-1	pancreas:	n/a
32	chr4:172219751-172219801	HAEpiC	amniotic membrane:	n/a
33	chr4:172219751-172219801	HCF	heart:	n/a
34	chr4:172219751-172219801	NHDF-neo	bronchial:	n/a
35	chr4:172219751-172219801	HPAEpiC	pulmonary alveolar:	n/a
36	chr4:172219751-172219801	RPTEC	kidney:	n/a
37	chr4:172219751-172219801	GM12891	blood:	n/a
38	chr4:172219751-172219801	PFSK-1	brain:	n/a
39	chr4:172219751-172219801	AG10803	skin:	n/a
40	chr4:172219751-172219801	NHBE	bronchial:	n/a
41	chr4:172219751-172219801	HEK293	kidney:	embryo
42	chr4:172219751-172219801	GM19239	blood:	n/a
43	chr4:172219751-172219801	ProgFib	skin:	n/a
44	chr4:172219751-172219801	BJ	skin:	n/a
45	chr4:172219751-172219801	A549	lung:	n/a
46	chr4:172219751-172219801	CMK	blood:	n/a
47	chr4:172219751-172219801	MCF-7	breast:	n/a
48	chr4:172219751-172219801	HUVEC	blood vessel:	n/a
49	chr4:172219751-172219801	PrEC	prostate:	n/a
50	chr4:172219751-172219801	HMEC	breast:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:172212656..172215279-chr4:172273980..172275669,2	K562	blood:
2	chr4:172215180..172217206-chr4:172338805..172340584,2	K562	blood:
3	chr4:172207640..172210235-chr4:172213745..172216390,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GALNTL6-3	chr4:172213931-172214064	ucscGeneNc_uc003isu_1
2	lnc-GALNTL6-3	chr4:172215603-172216886	ucscGeneNc_uc003isu_1
3	lnc-GALNTL6-3	chr4:172213554-172213624	ucscGeneNc_uc003isu_1

No data

Variant related genes	Relation type
ENSG00000248339	TF binding region
ENSG00000248339	CpG island

Extended variants
information (count: 176 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:176 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs148171849	chr4:172213591-172213592	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs58559254	chr4:172213594-172213595	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs184786143	chr4:172213596-172213597	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs552880244	chr4:172213601-172213602	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs190536375	chr4:172213605-172213606	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs570562367	chr4:172213939-172213940	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs566640257	chr4:172213954-172213955	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs144080372	chr4:172213993-172213994	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs546459999	chr4:172214011-172214012	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs553157323	chr4:172214026-172214027	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs116736351	chr4:172214044-172214045	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs541730633	chr4:172214058-172214059	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs558989048	chr4:172214063-172214064	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs575180333	chr4:172214113-172214114	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs544226976	chr4:172214145-172214146	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs564306453	chr4:172214157-172214158	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs571185972	chr4:172214160-172214161	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs547911052	chr4:172214180-172214181	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs540339595	chr4:172214188-172214189	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs560737332	chr4:172214191-172214192	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs529465495	chr4:172214193-172214194	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs6833288	chr4:172214200-172214201	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs140916350	chr4:172214207-172214208	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs532029594	chr4:172214215-172214216	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs186922724	chr4:172214266-172214267	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs144473551	chr4:172214300-172214301	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs80173962	chr4:172214317-172214318	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs557023002	chr4:172214395-172214396	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs546338103	chr4:172214397-172214398	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs72981910	chr4:172214412-172214413	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs76595577	chr4:172214442-172214443	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs190009165	chr4:172214443-172214444	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs573938726	chr4:172214461-172214462	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs575189146	chr4:172214509-172214510	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs537714619	chr4:172214515-172214516	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs558153521	chr4:172214524-172214525	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs147485166	chr4:172214543-172214544	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs570383641	chr4:172214550-172214551	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs560419944	chr4:172214571-172214572	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs181059929	chr4:172214582-172214583	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs542657236	chr4:172214603-172214604	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs543279915	chr4:172214623-172214624	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs563039963	chr4:172214638-172214639	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs552974812	chr4:172214706-172214707	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs532307508	chr4:172214726-172214727	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs551742745	chr4:172214747-172214748	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs72981912	chr4:172214750-172214751	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs532829871	chr4:172214755-172214756	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs139279878	chr4:172214760-172214761	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs80185504	chr4:172214893-172214894	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:70)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Wilms tumour	21544195	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Breast cancer	16272173	CNVD
Breast cancer	17133270	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Testicular germ cell tumor	18059402	CNVD
Ovarian cancer	22174824	CNVD
Olfactory neuroblastoma	18408657	CNVD
Breast cancer	21785460	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Ewing''s sarcoma	17952124	CNVD
Breast cancer	21633010	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20581869	CNVD
Hepatocellular carcinoma	16750200	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
abnormal development	18461090	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Neuroblastoma	16790693	CNVD
Schizophrenia	23813976	CNVD
Lung cancer	16773561	CNVD
Colorectal cancer	16774939	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	22127048	CNVD
Glioblastoma multiforme	22286061	CNVD
Neuroblastoma	21899760	CNVD
Gastric adenocarcinoma	19115996	CNVD

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:172214000-172215600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:172214600-172215400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:172214800-172215000	Active TSS	Adipose Nuclei	Adipose
4	chr4:172215000-172215600	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr4:172215600-172216000	Enhancers	Adipose Nuclei	Adipose
6	chr4:172219200-172219800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:172219200-172219800	Active TSS	Placenta	Placenta

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